2faq: Difference between revisions

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 ==Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain with ATP and Manganese==
-<StructureSection load='2faq' size='340' side='right' caption='[[2faq]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='2faq' size='340' side='right'caption='[[2faq]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2faq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_aeruginosus"_(schroeter_1872)_trevisan_1885 "bacillus aeruginosus" (schroeter 1872) trevisan 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FAQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FAQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2faq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FAQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FAQ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2fao|2fao]], [[2far|2far]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2faq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2faq OCA], [http://pdbe.org/2faq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2faq RCSB], [http://www.ebi.ac.uk/pdbsum/2faq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2faq ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2faq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2faq OCA], [https://pdbe.org/2faq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2faq RCSB], [https://www.ebi.ac.uk/pdbsum/2faq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2faq ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/LIGD_PSEAE LIGD_PSEAE] With Ku probably forms a non-homologous end joining (NHEJ) repair enzyme, which repairs dsDNA breaks (DSB) with reduced fidelity. Acts as a DNA ligase on singly nicked dsDNA, fills dsDNA gaps (3- or 4- nucleotide gaps, prefers a 5'-phosphate at the gap distal end, prefers dNTPs over rNTPs) (PubMed:20018881), has DNA-directed DNA polymerase activity (templated primer extension) and DNA-directed RNA polymerase activity (PubMed:15897197), adds 1 or 2 non-templated rNTP (or less well dNTP) to ssDNA or blunt-end dsDNA (primer extension). Has 3' resection activity, removing 3'-rNMPs from DNA using its 3'-ribonuclease and 3'-phosphatase activities sequentially. Resection requires a 2'-OH in the penultimate nucleoside position (i.e. a ribo- not deoxyribonucleoside) (PubMed:15897197), although the 3'-phosphatase activity does not, and its specific activity is 16-fold higher on a DNA substrate (PubMed:16046407). On appropriate substrates will extend a DNA primer to the end of the template strand and then incorporate a non-templated nucleotide.<ref>PMID:15897197</ref> <ref>PMID:16046407</ref> <ref>PMID:20018881</ref>   The preference of the polymerase domain for rNTPs over dNTPs may be advantageous in quiescent cells where the dNTP pool may be limiting.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fa/2faq_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fa/2faq_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 27: / Line 29: @@
 </div>
 <div class="pdbe-citations 2faq" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[DNA ligase 3D structures|DNA ligase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Aniukwu, J]]
+[[Category: Large Structures]]
-[[Category: Glickman, M S]]
+[[Category: Pseudomonas aeruginosa]]
-[[Category: Lima, C D]]
+[[Category: Aniukwu J]]
-[[Category: Nandakumar, J]]
+[[Category: Glickman MS]]
-[[Category: Shuman, S]]
+[[Category: Lima CD]]
-[[Category: Wang, L K]]
+[[Category: Nandakumar J]]
-[[Category: Zhu, H]]
+[[Category: Shuman S]]
-[[Category: Atp]]
+[[Category: Wang LK]]
-[[Category: Hydrolase-transferase complex]]
+[[Category: Zhu H]]
-[[Category: Ligase]]
-[[Category: Nhej]]
-[[Category: Polymerase]]
-[[Category: Primase]]